You'd only get the original calculated value if you've already executed getCalculatedValue() for that cell prior to overriding cell values, because PHPExcel maintains a cell cache of previously calculated values for each cell and uses that if available.
Either don't call getCalculatedValue() before populating your cells, or flush the cache using PHPExcel_Calculation::getInstance()->clearCalculationCache() before your subsequent call to getCalculatedValue();

Take a look at the Quadratic.php example in /Tests which does pretty much what you're asking